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Ontologizer is a tool for identifying enriched Gene Ontology terms in lists of names of genes or gene products.

Java 96.50% R 0.78% HTML 1.70% Shell 0.34% Makefile 0.25% CSS 0.27% JavaScript 0.07% Python 0.07% Dockerfile 0.03%

ontologizer's Introduction

Ontologizer

Ontologizer is a tool for identifying enriched Gene Ontology terms in lists of names of genes or gene products. It is available as a Java program for both UI and command line usage as well as JavaScript version that can be conveniently run in modern Web browsers. Look at http://ontologizer.de for details and binary distribution.

Building

Ontologizer's build process is driven by Maven. You also need to install '''pandoc''' (https://pandoc.org/) before proceeding, as this is not handled by Maven. After cloning and checking out the source repository via

$ git clone --recurse-submodules https://github.com/sba1/ontologizer

you can start the build procedure via

$ cd ontologizer.parent
$ mvn package

When the build breaks due to bugs in Javadocs, add -Dmaven.javadoc.skip=true to the previous command and file an Issue. Similiary, if tests break the build you can add -DskipTests to skip the execution of the tests.

If successful, the command line version can be found in ontologizer.cmdline and the UI version in the ontologizer.gui modules in the respective target folders.

For instance, still being in the ontologizer.parent folder, you can start the GUI version by

$ cd ../ontologizer.gui/target
$ java -jar Ontologizer-jar-with-dependencies.jar

The Ontologizer-jar-with-dependencies.jar includes all dependencies, incl. SWT for your platform.

API - ontologizerlib

The core of Ontologizer can be in principle used by other applications, although the API is rather dumb. Please have a look at the https://github.com/ontologizer/ontologizerlib for the library project. The project is currently used in Ontologizer via directly importing the source. This simplifies the coordinated development of both projects.

ontologizer's People

Contributors

Stargazers

Watchers

Forkers

visze moriarty balhoff holtgrewe johntiger1 ornrocha desaurabh 790675356

ontologizer's Issues

Gene names from enrichmed GO term

I ran MGSA from Ontologizer and got the list of enriched terms. However, I am also interested in gene names that are associated with the enriched terms. Is there any way to retrieve this information.

GO in three categories: (1) Molecular Function (2) Biological Process (3) Cellular component.

Can Ontologizer report the GO enrichment in three categories: (1) Molecular Function (2) Biological Process (3) Cellular component. Currently, entire results are reported as one single list.

Add ability to check for overrepresentation of HPO terms.

Use HPO analogously to GO term overrepresentation.

mvn package failing

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] ontologizer.parent ................................. SUCCESS [ 0.007 s]
[INFO] ontologizer ........................................ SUCCESS [01:05 min]
[INFO] ontologizer.dataprep ............................... SUCCESS [ 19.301 s]
[INFO] ontologizer.obogen ................................. SUCCESS [ 0.325 s]
[INFO] ontologizer.jmh .................................... SUCCESS [ 15.836 s]
[INFO] ontologizer.changelog .............................. SUCCESS [ 0.247 s]
[INFO] ontologizer.grappa ................................. SUCCESS [ 1.301 s]
[INFO] ontologizer.svd .................................... SUCCESS [ 0.555 s]
[INFO] ontologizer.benchmark .............................. SUCCESS [ 1.809 s]
[INFO] ontologizer.tests .................................. SUCCESS [ 18.764 s]
[INFO] ontologizer.gui .................................... SUCCESS [ 45.634 s]
[INFO] ontologizer.cmdline ................................ FAILURE [ 0.449 s]
[INFO] ontologizer.cmdline.printopts ...................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:49 min
[INFO] Finished at: 2017-07-28T17:24:31-04:00
[INFO] Final Memory: 59M/447M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (default) on project ontologizer.cmdline: Command execution failed.: Cannot run program "pandoc" (in directory "C:\Users\johnp\Desktop\git_stuff\seb_onto\ontologizer\ontologizer.cmdline\doc"): CreateProcess error=2, The system cannot find the file specified -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :ontologizer.cmdline

TermID.java

Line 42: import ontologizer.ontology.TermID;

https://github.com/sba1/ontologizer/blob/master/ontologizer.tests/src/ontologizer/sets/tests/StudySetTest.java

The import appears to reference a TermID.java class. However, it seems that TermID.java has been moved to ontolib? At any rate, I cannot find TermID.java here. Any help would be appreciated. Thanks.

Command line version should support specification of sub ontology and subset.

License?

Which license is ontologizer source code released under?

Thanks,
Seb

ELIM module not working

I am trying to look for over representation of GO terms in my Arabidopsis dataset. I have one background AGI set and 3 foreground AGI sets.

I can successfully use the Parent-Child Intersection approach with no issues. However, when I plug the data into The Ontologizer and use the ELIM setting it gets stuck on the first set and nothing is displayed in the popup window.

Any idea what the issue is?

[question] Slim View

Sorry for the simple question, but I want to confirm, what is a "slim view" of a graph? Is it just the regular DirectedGraph, except using smaller primitives for faster performance?

Fix javadocs to work with java8

java8 is stricter when it comes to javadocs. Trying to build @drseb's branch with mvn:

ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.10.3:jar (generate-javadoc-jar) on project ontologizer: MavenReportException: Error while generating Javadoc:
[ERROR] Exit code: 1 - /Users/cjm/repos/drseb/ontologizer/ontologizer/src/ontologizer/AbstractStudySetResult.java:40: warning: no description for @param
[ERROR] * @param goTermID

This seems to be one possible workaround:
http://www.locked.de/2015/04/05/how-to-ignore-maven-javadoc-errors-in-java-8/

But doesn't seem to work for me

Anaconda package

Dear Author,

I would like to use Ontologizer in a bigger pipeline I build. Every step is in executed in a conda environment with specified libs and packages to ease re-runing the tool and avoid installation/dependency problems. Could you please consider building an Ontologizer conda package and uploading it to anaconda cloud as described here?